NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM143507 Query DataSets for GSM143507
Status Public on Feb 01, 2007
Title Thatcher_Lr34 (resistant), rust inoculated distal leaf, replication 3
Sample type RNA
 
Source name Fully expanded wheat flag leaves, distal half, rust inoculated
Organism Triticum aestivum
Characteristics Genotype: Thatcher_Lr34
Growth stage: mid-anthesis
Treatment protocol Plants were heavily inoculated with the Puccinia triticina race MFBL suspended in Soltrol 170 light oil (Chevron Phillips Chemical Company, The Woodlands, TX), and were then incubated in a mist chamber with 100% RH for 12 hr. The plants were returned to the growth chamber until sampling at 48 hr after removal from the mist chamber.
Growth protocol Plants were grown in 4-liter pots in growth chamber (Conviron PGW-36) under 15C night/20C day (+/- 1C) with a 16 hr photoperiod. Pots were fertilized at planting with 5 g/pot 14-14-14 Osmocote (The Scotts Company, Marysville, OH) and thereafter every two weeks with 0.5 g/pot 15-30-15 Miracle-Gro All Purpose Plant Food (Scott's Miracle-Gro Products, Inc., Marysville, OH) and 0.1 ml/pot Fertilome Chelated Liquid Iron and Other Micronutrients (Voluntary Purchasing Groups, Inc., Bonham, TX).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip wheat Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Wheat fully expanded flag leaf, rust inoculated distal half, biological replication 3.
Data processing The data were analyzed with Affymetrix GCOS software using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Nov 02, 2006
Last update date Nov 08, 2006
Contact name Jianfa Bai
E-mail(s) jbai@ksu.edu
Phone 785-532-4332
Organization name Kansas State University
Department Diagnostic Medicine and Pathobiology
Street address 1800 Denison Ave
City Manhattan
State/province KS
ZIP/Postal code 66506-5502
Country USA
 
Platform ID GPL3802
Series (1)
GSE6227 Expression data from rust or mock inoculated, fully expanded flag leaf halves

Data table header descriptions
ID_REF Affymetrix probe set ID
VALUE GCOS-calculated signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 686.0 P 0.000662
AFFX-BioB-M_at 826.0 P 0.000147
AFFX-BioB-3_at 493.3 P 0.000169
AFFX-BioC-5_at 2080.3 P 0.000052
AFFX-BioC-3_at 2053.0 P 0.000052
AFFX-BioDn-5_at 3652.9 P 0.000044
AFFX-BioDn-3_at 7896.5 P 0.000052
AFFX-CreX-5_at 22641.0 P 0.000052
AFFX-CreX-3_at 30532.9 P 0.000044
AFFX-DapX-5_at 1636.6 P 0.000052
AFFX-DapX-M_at 2454.0 P 0.000081
AFFX-DapX-3_at 2926.4 P 0.000060
AFFX-LysX-5_at 113.5 P 0.000340
AFFX-LysX-M_at 183.9 P 0.030976
AFFX-LysX-3_at 510.3 P 0.000052
AFFX-PheX-5_at 247.7 P 0.000297
AFFX-PheX-M_at 241.4 P 0.003212
AFFX-PheX-3_at 350.2 P 0.000390
AFFX-ThrX-5_at 365.2 P 0.000340
AFFX-ThrX-M_at 536.4 P 0.000044

Total number of rows: 61290

Table truncated, full table size 2139 Kbytes.




Supplementary file Size Download File type/resource
GSM143507.CEL.gz 4.9 Mb (ftp)(http) CEL

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap